List of works - Marnix H Medema

A Pressure Test to Make 10 Molecules in 90 Days: External Evaluation of Methods to Engineer Biology

scientific article published on 26 February 2018

A biaryl-linked tripeptide from Planomonospora reveals a widespread class of minimal RiPP gene clusters ⬇️

scientific article published on 10 December 2020

A community resource for paired genomic and metabolomic data mining

scientific article published in 2021

A computational framework for systematic exploration of biosynthetic diversity from large-scale genomic data

A computational framework to explore large-scale biosynthetic diversity

scientific article published on 25 November 2019

A genetical metabolomics approach for bioprospecting plant biosynthetic gene clusters

scientific article published on 02 April 2019

A predicted physicochemically distinct sub-proteome associated with the intracellular organelle of the anammox bacterium Kuenenia stuttgartiensis

scientific article

A standardized workflow for submitting data to the Minimum Information about a Biosynthetic Gene cluster (MIBiG) repository: prospects for research-based educational experiences

article

A systematic computational analysis of biosynthetic gene cluster evolution: lessons for engineering biosynthesis

scientific article

ARTS 2.0: feature updates and expansion of the Antibiotic Resistant Target Seeker for comparative genome mining

scientific article published on 19 May 2020

An isotopic labeling approach linking natural products with biosynthetic gene clusters

scientific article published on 30 December 2021

Analysis of the Pseudouridimycin Biosynthetic Pathway Provides Insights into the Formation of C-nucleoside Antibiotics ⬇️

scientific article published on 15 March 2018

Artificial intelligence for natural product drug discovery ⬇️

scientific article from 2023

Assessing Specialized Metabolite Diversity in the Cosmopolitan Plant Genus Euphorbia L

scientific article published on 02 July 2019

Author Correction: Compendium of specialized metabolite biosynthetic diversity encoded in bacterial genomes

correction of a scholarly article

Author Correction: The planctomycete Stieleria maiorica Mal15T employs stieleriacines to alter the species composition in marine biofilms

scientific article published on 21 September 2020

Author Correction: The planctomycete Stieleria maiorica Mal15T employs stieleriacines to alter the species composition in marine biofilms

scientific article published on 31 August 2020

Benefiting from big data in natural products: importance of preserving foundational skills and prioritizing data quality

scientific article published on 04 November 2021

BiG-FAM: the biosynthetic gene cluster families database

scientific article published on 03 October 2020

BiG-MAP: an Automated Pipeline To Profile Metabolic Gene Cluster Abundance and Expression in Microbiomes

scientific article published on 28 September 2021

BiG-SLiCE: A highly scalable tool maps the diversity of 1.2 million biosynthetic gene clusters

scientific article published in January 2021

Bioinformatics approaches and software for detection of secondary metabolic gene clusters.

scientific article published on January 2012

BiosyntheticSPAdes: reconstructing biosynthetic gene clusters from assembly graphs

scientific article published on 03 June 2019

Coevolution-based prediction of protein-protein interactions in polyketide biosynthetic assembly lines

scientific article published on 27 June 2020

Collaborating with Undergraduates To Contribute to Biochemistry Community Resources

scientific article published on 19 October 2017

Comparative genome-scale metabolic modeling of actinomycetes: The topology of essential core metabolism

article

Compendium of specialized metabolite biosynthetic diversity encoded in bacterial genomes

scientific article published in 2022

Complete genome sequence of the frog pathogen Mycobacterium ulcerans ecovar Liflandii

scientific article

Comprehensive curation and analysis of fungal biosynthetic gene clusters of published natural products.

scientific article

Comprehensive mass spectrometry-guided phenotyping of plant specialized metabolites reveals metabolic diversity in the cosmopolitan plant family Rhamnaceae

scientific article published on 25 March 2019

Comprehensive mass spectrometry-guided plant specialized metabolite phenotyping reveals metabolic diversity in the cosmopolitan plant family Rhamnaceae

scientific article published on 7 November 2018

Computational Applications in Secondary Metabolite Discovery (CAiSMD): an online workshop

scientific article

Computational Genomics of Specialized Metabolism: from Natural Product Discovery to Microbiome Ecology

scientific article published on 6 March 2018

Computational approaches to natural product discovery

scientific article

Computational genomic discovery of diverse gene clusters harbouring Fe-S flavoenzymes in anaerobic gut microbiota

scientific article published on 14 May 2020

Computational genomic identification and functional reconstitution of plant natural product biosynthetic pathways.

scientific article published on 20 June 2016

Computational identification of co-evolving multi-gene modules in microbial biosynthetic gene clusters

article

Computational strategies for genome-based natural product discovery and engineering in fungi

scientific article

Computational tools for the synthetic design of biochemical pathways

scientific article published on 23 January 2012

Computer-aided re-engineering of nonribosomal peptide and polyketide biosynthetic assembly lines

scientific article published on 01 July 2019

Cultivation and functional characterization of 79 planctomycetes uncovers their unique biology

scientific article published on 18 November 2019

Denitrifying bacteria anaerobically oxidize methane in the absence of Archaea.

scientific article published on 20 August 2008

Design-based re-engineering of biosynthetic gene clusters: plug-and-play in practice

scientific article

Detecting Sequence Homology at the Gene Cluster Level with MultiGeneBlast ⬇️

scientific article published on February 14, 2013

Did a plant-herbivore arms race drive chemical diversity in Euphorbia?

scientific article published on 15 May 2018

Discovery and biosynthesis of cyclic plant peptides via autocatalytic cyclases

scientific article published in 2021

Disentangling the genetic basis of rhizosphere microbiome assembly in tomato

scientific article published on 01 January 2022

Dissecting Disease-Suppressive Rhizosphere Microbiomes by Functional Amplicon Sequencing and 10× Metagenomics

scientific article published on 08 June 2021

Draft Genome Sequence of a Porcine Commensal, Rothia nasimurium, Encoding a Nonribosomal Peptide Synthetase Predicted To Produce the Ionophore Antibiotic Valinomycin

scientific article published on June 2017

Drivers of metabolic diversification: how dynamic genomic neighbourhoods generate new biosynthetic pathways in the Brassicaceae

scientific article published on 26 November 2019

Ecology and genomics of Actinobacteria: new concepts for natural product discovery

scientific article published on 01 June 2020

Editorial: Synthetic biology and bioinformatics

scientific article published on 20 July 2016

Empowering natural product science with AI: leveraging multimodal data and knowledge graphs

Erratum: Indexing the Pseudomonas specialized metabolome enabled the discovery of poaeamide B and the bananamides

scientific article published on 23 January 2017

Evolution and Diversity of Biosynthetic Gene Clusters in Fusarium.

scientific article published on 5 June 2018

Evolution of combinatorial diversity in trans-acyltransferase polyketide synthase assembly lines across bacteria ⬇️

scientific article published on 03 March 2021

Expansion of RiPP biosynthetic space through integration of pan-genomics and machine learning uncovers a novel class of lantibiotics ⬇️

scientific article published on 22 December 2020

Exploiting plug-and-play synthetic biology for drug discovery and production in microorganisms

article

Exploration and exploitation of the environment for novel specialized metabolites.

scientific article published on 14 February 2018

Exploring the Interspecific Interactions and the Metabolome of the Soil Isolate Hylemonella gracilis

scientific article published in 2023

FERMO: a Dashboard for Streamlined Rationalized Prioritization of Molecular Features from Mass Spectrometry Data

scientific article published on 22 December 2022

Functional Exchangeability of Oxidase and Dehydrogenase Reactions in the Biosynthesis of Hydroxyphenylglycine, a Nonribosomal Peptide Building Block.

scientific article published on 9 March 2015

Fungi population metabolomics and molecular network study reveal novel biomarkers for early detection of aflatoxigenic Aspergillus species

scientific article published in 2022

Genome-based exploration of the specialized metabolic capacities of the genus Rhodococcus

scientific article

Genome-wide analysis of bacterial determinants of plant growth promotion and induced systemic resistance by Pseudomonas fluorescens

scientific article published on 11 September 2017

Genome-wide gene expression changes in an industrial clavulanic acid overproduction strain of Streptomyces clavuligerus ⬇️

scientific article published on 2 November 2010

Genomic Identification and Analysis of Specialized Metabolite Biosynthetic Gene Clusters in Plants Using PlantiSMASH

scientific article published on 01 January 2018

Genomic mutational analysis of the impact of the classical strain improvement program on β-lactam producing Penicillium chrysogenum

scientific article published on 14 November 2015

Global analysis of adenylate-forming enzymes reveals β-lactone biosynthesis pathway in pathogenic Nocardia

scientific article published on 21 August 2020

HEx: A heterologous expression platform for the discovery of fungal natural products ⬇️

scientific article published on 11 April 2018

HEx: a heterologous expression platform for the discovery of fungal natural products

Indexing the Pseudomonas specialized metabolome enabled the discovery of poaeamide B and the bananamides ⬇️

scientific article published on 31 October 2016

Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters ⬇️

scientific article published in July 2014

Integrative omics approaches for biosynthetic pathway discovery in plants

scientific article published in January 2022

Involvement of Burkholderiaceae and sulfurous volatiles in disease-suppressive soils

scientific article published on 13 June 2018

Leucanicidin and Endophenasides Result from Methyl-Rhamnosylation by the Same Tailoring Enzymes in Kitasatospora sp. MBT66.

scientific article published on 16 December 2015

Linking genomics and metabolomics to chart specialized metabolic diversity

scientific article published on 12 May 2020

MIBiG 2.0: a repository for biosynthetic gene clusters of known function

scientific article published on 01 January 2020

MIBiG 3.0: a community-driven effort to annotate experimentally validated biosynthetic gene clusters

scientific article published on 18 November 2022

MIBiG 4.0: advancing biosynthetic gene cluster curation through global collaboration

scientific article published on 9 December 2024

MS/MS networking guided analysis of molecule and gene cluster families.

scientific article published on 24 June 2013

Mechanisms and evolution of control logic in prokaryotic transcriptional regulation.

scientific article published on September 2009

Metabolome-guided genome mining of RiPP natural products

scientific article published in August 2023

Metabolomics methods for the synthetic biology of secondary metabolism

scientific article

Microbial and volatile profiling of soils suppressive to Fusarium culmorum of wheat

scientific article published on 19 February 2020

Microbial natural product databases: moving forward in the multi-omics era

scientific article published on 28 August 2020

Minimum Information about a Biosynthetic Gene cluster.

scientific article published on August 2015

Mining bacterial genomes to reveal secret synergy

scientific article published in Journal of Biological Chemistry

Mining genomes to illuminate the specialized chemistry of life

scientific article published in 2021

Mining prokaryotes for antimicrobial compounds: from diversity to function

scientific article published on 11 April 2017

MolNetEnhancer: Enhanced Molecular Networks by Integrating Metabolome Mining and Annotation Tools

scientific article published on 16 July 2019

MolNetEnhancer: enhanced molecular networks by integrating metabolome mining and annotation tools

scientific article published on 31 May 2019

MultiMetEval: comparative and multi-objective analysis of genome-scale metabolic models

scientific article

NRPSpredictor2--a web server for predicting NRPS adenylation domain specificity

scientific article

Omics-based strategies to discover novel classes of RiPP natural products

scientific article published on 28 December 2020

PIKAChU: a Python-based informatics kit for analysing chemical units

scientific article published on 07 June 2022

Pan-genome analysis and ancestral state reconstruction of class halobacteria: probability of a new super-order

scientific article published on 03 December 2020

Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome

scientific article published on 01 November 2019

Pep2Path: automated mass spectrometry-guided genome mining of peptidic natural products

scientific article

RRE-Finder: a Genome-Mining Tool for Class-Independent RiPP Discovery

scientific article published on 01 September 2020

Recent development of antiSMASH and other computational approaches to mine secondary metabolite biosynthetic gene clusters.

scientific article

Road MAPs to engineer host microbiomes

scientific article published on 2 December 2017

SANDPUMA: Ensemble Predictions of Nonribosomal Peptide Chemistry Reveals Biosynthetic Diversity across Actinobacteria

scientific article published on 19 June 2017

Standardization for natural product synthetic biology.

scientific article published on 17 June 2016

Structure and function of the global topsoil microbiome

scientific article published in Nature

Synthetic Biology in Streptomyces Bacteria

scholarly article by Marnix H Medema et al published 2011 in Methods in Enzymology

The Minimum Information About A Biosynthetic Gene Cluster Standard as a Means of Organizing Bioinformatic Data

scientific article published in 2018

The Natural Products Atlas: An Open Access Knowledge Base for Microbial Natural Products Discovery

scientific article published on 14 November 2019

The antiSMASH database version 2: a comprehensive resource on secondary metabolite biosynthetic gene clusters

article

The antiSMASH database version 3: increased taxonomic coverage and new query features for modular enzymes

scientific article published on 05 November 2020

The antiSMASH database, a comprehensive database of microbial secondary metabolite biosynthetic gene clusters

scientific article published on 24 October 2016

The future of industrial antibiotic production: from random mutagenesis to synthetic biology

scientific article published on July 2011

The gutSMASH web server: automated identification of primary metabolic gene clusters from the gut microbiota

scientific article published on 01 July 2021

The planctomycete Stieleria maiorica Mal15T employs stieleriacines to alter the species composition in marine biofilms

scientific article published on 12 June 2020

The sequence of a 1.8-mb bacterial linear plasmid reveals a rich evolutionary reservoir of secondary metabolic pathways

scientific article published on 12 July 2010

The year 2020 in natural product bioinformatics: an overview of the latest tools and databases

scientific article published in 2021

Towards the sustainable discovery and development of new antibiotics

scientific article published in 2021

Unearthing a sesterterpene biosynthetic repertoire in the Brassicaceae through genome mining reveals convergent evolution

scientific article published on 3 July 2017

antiSMASH

antiSMASH 2.0--a versatile platform for genome mining of secondary metabolite producers

scientific article published on 3 June 2013

antiSMASH 3.0-a comprehensive resource for the genome mining of biosynthetic gene clusters

scientific article published on 6 May 2015

antiSMASH 4.0-improvements in chemistry prediction and gene cluster boundary identification

scientific article published on 28 April 2017

antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline

scientific article published on 01 July 2019

antiSMASH 6.0: improving cluster detection and comparison capabilities

scientific article published in 2021

antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences

scientific article published on 14 June 2011

iPRESTO: automated discovery of biosynthetic sub-clusters linked to specific natural product substructures

scientific article published on 6 August 2022

luxR Homolog-Linked Biosynthetic Gene Clusters in Proteobacteria

scientific article published on 27 March 2018

plantiSMASH: automated identification, annotation and expression analysis of plant biosynthetic gene clusters

scientific article

List of works by Marnix H Medema

A Pressure Test to Make 10 Molecules in 90 Days: External Evaluation of Methods to Engineer Biology

A biaryl-linked tripeptide from Planomonospora reveals a widespread class of minimal RiPP gene clusters ⬇️

A community resource for paired genomic and metabolomic data mining

A computational framework for systematic exploration of biosynthetic diversity from large-scale genomic data

A computational framework to explore large-scale biosynthetic diversity

A genetical metabolomics approach for bioprospecting plant biosynthetic gene clusters

A predicted physicochemically distinct sub-proteome associated with the intracellular organelle of the anammox bacterium Kuenenia stuttgartiensis

A standardized workflow for submitting data to the Minimum Information about a Biosynthetic Gene cluster (MIBiG) repository: prospects for research-based educational experiences

A systematic computational analysis of biosynthetic gene cluster evolution: lessons for engineering biosynthesis

ARTS 2.0: feature updates and expansion of the Antibiotic Resistant Target Seeker for comparative genome mining

An isotopic labeling approach linking natural products with biosynthetic gene clusters

Analysis of the Pseudouridimycin Biosynthetic Pathway Provides Insights into the Formation of C-nucleoside Antibiotics ⬇️

Artificial intelligence for natural product drug discovery ⬇️

Assessing Specialized Metabolite Diversity in the Cosmopolitan Plant Genus Euphorbia L

Author Correction: Compendium of specialized metabolite biosynthetic diversity encoded in bacterial genomes

Author Correction: The planctomycete Stieleria maiorica Mal15T employs stieleriacines to alter the species composition in marine biofilms

Author Correction: The planctomycete Stieleria maiorica Mal15T employs stieleriacines to alter the species composition in marine biofilms

Benefiting from big data in natural products: importance of preserving foundational skills and prioritizing data quality

BiG-FAM: the biosynthetic gene cluster families database

BiG-MAP: an Automated Pipeline To Profile Metabolic Gene Cluster Abundance and Expression in Microbiomes

BiG-SLiCE: A highly scalable tool maps the diversity of 1.2 million biosynthetic gene clusters

Bioinformatics approaches and software for detection of secondary metabolic gene clusters.

BiosyntheticSPAdes: reconstructing biosynthetic gene clusters from assembly graphs

Coevolution-based prediction of protein-protein interactions in polyketide biosynthetic assembly lines

Collaborating with Undergraduates To Contribute to Biochemistry Community Resources

Comparative genome-scale metabolic modeling of actinomycetes: The topology of essential core metabolism

Compendium of specialized metabolite biosynthetic diversity encoded in bacterial genomes

Complete genome sequence of the frog pathogen Mycobacterium ulcerans ecovar Liflandii

Comprehensive curation and analysis of fungal biosynthetic gene clusters of published natural products.

Comprehensive mass spectrometry-guided phenotyping of plant specialized metabolites reveals metabolic diversity in the cosmopolitan plant family Rhamnaceae

Comprehensive mass spectrometry-guided plant specialized metabolite phenotyping reveals metabolic diversity in the cosmopolitan plant family Rhamnaceae

Computational Applications in Secondary Metabolite Discovery (CAiSMD): an online workshop

Computational Genomics of Specialized Metabolism: from Natural Product Discovery to Microbiome Ecology

Computational approaches to natural product discovery

Computational genomic discovery of diverse gene clusters harbouring Fe-S flavoenzymes in anaerobic gut microbiota

Computational genomic identification and functional reconstitution of plant natural product biosynthetic pathways.

Computational identification of co-evolving multi-gene modules in microbial biosynthetic gene clusters

Computational strategies for genome-based natural product discovery and engineering in fungi

Computational tools for the synthetic design of biochemical pathways

Computer-aided re-engineering of nonribosomal peptide and polyketide biosynthetic assembly lines

Cultivation and functional characterization of 79 planctomycetes uncovers their unique biology

Denitrifying bacteria anaerobically oxidize methane in the absence of Archaea.

Design-based re-engineering of biosynthetic gene clusters: plug-and-play in practice

Detecting Sequence Homology at the Gene Cluster Level with MultiGeneBlast ⬇️

Did a plant-herbivore arms race drive chemical diversity in Euphorbia?

Discovery and biosynthesis of cyclic plant peptides via autocatalytic cyclases

Disentangling the genetic basis of rhizosphere microbiome assembly in tomato

Dissecting Disease-Suppressive Rhizosphere Microbiomes by Functional Amplicon Sequencing and 10× Metagenomics

Draft Genome Sequence of a Porcine Commensal, Rothia nasimurium, Encoding a Nonribosomal Peptide Synthetase Predicted To Produce the Ionophore Antibiotic Valinomycin

Drivers of metabolic diversification: how dynamic genomic neighbourhoods generate new biosynthetic pathways in the Brassicaceae

Ecology and genomics of Actinobacteria: new concepts for natural product discovery

Editorial: Synthetic biology and bioinformatics

Empowering natural product science with AI: leveraging multimodal data and knowledge graphs

Erratum: Indexing the Pseudomonas specialized metabolome enabled the discovery of poaeamide B and the bananamides

Evolution and Diversity of Biosynthetic Gene Clusters in Fusarium.

Evolution of combinatorial diversity in trans-acyltransferase polyketide synthase assembly lines across bacteria ⬇️

Expansion of RiPP biosynthetic space through integration of pan-genomics and machine learning uncovers a novel class of lantibiotics ⬇️

Exploiting plug-and-play synthetic biology for drug discovery and production in microorganisms

Exploration and exploitation of the environment for novel specialized metabolites.

Exploring the Interspecific Interactions and the Metabolome of the Soil Isolate Hylemonella gracilis

FERMO: a Dashboard for Streamlined Rationalized Prioritization of Molecular Features from Mass Spectrometry Data

Functional Exchangeability of Oxidase and Dehydrogenase Reactions in the Biosynthesis of Hydroxyphenylglycine, a Nonribosomal Peptide Building Block.

Fungi population metabolomics and molecular network study reveal novel biomarkers for early detection of aflatoxigenic Aspergillus species

Genome-based exploration of the specialized metabolic capacities of the genus Rhodococcus

Genome-wide analysis of bacterial determinants of plant growth promotion and induced systemic resistance by Pseudomonas fluorescens

Genome-wide gene expression changes in an industrial clavulanic acid overproduction strain of Streptomyces clavuligerus ⬇️

Genomic Identification and Analysis of Specialized Metabolite Biosynthetic Gene Clusters in Plants Using PlantiSMASH

Genomic mutational analysis of the impact of the classical strain improvement program on β-lactam producing Penicillium chrysogenum

Global analysis of adenylate-forming enzymes reveals β-lactone biosynthesis pathway in pathogenic Nocardia

HEx: A heterologous expression platform for the discovery of fungal natural products ⬇️

HEx: a heterologous expression platform for the discovery of fungal natural products

Indexing the Pseudomonas specialized metabolome enabled the discovery of poaeamide B and the bananamides ⬇️

Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters ⬇️

Integrative omics approaches for biosynthetic pathway discovery in plants

Involvement of Burkholderiaceae and sulfurous volatiles in disease-suppressive soils

Leucanicidin and Endophenasides Result from Methyl-Rhamnosylation by the Same Tailoring Enzymes in Kitasatospora sp. MBT66.

Linking genomics and metabolomics to chart specialized metabolic diversity

MIBiG 2.0: a repository for biosynthetic gene clusters of known function

MIBiG 3.0: a community-driven effort to annotate experimentally validated biosynthetic gene clusters